Workshop Description
This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.
Day 1
We will demonstrate the 16S rRNA gene analysis using QIIME
- Run QIIME on Hoffman2 or local
- Sequence data preparation
- Operational Taxonomic Units (OTU) picking, Taxonomic assignment & inferring phylogeny
Slides for day 1 can be found here.
Day 2
We will demonstrate the 16S rRNA gene analysis using QIIME
- Microbiome diversity analyses
Slides for day 2 can be found here.
Day 3
On day 3 we will learn functional analyses of the microbiome
Slides for day 3 can be found here.
Workshop Materials
- Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
- We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.
Instructor
Baochen Shi, Ph.D., is a postdoc working with Dr. Huiying Li in the department of Molecular and Medical Pharmacology. By studying genomes and transcriptomes of the microorganisms living inside and on the humans, he aims to understand how human microbiome play a role in health and disease. Prior to joining UCLA, he completed his Ph.D. in the bioinformatics lab of Prof. Runsheng Chen in the Institute of Biophysics, Chinese Academy of Sciences.
Email: biosbc@ucla.edu
Reviews
I’m glad that you actually have to change some file names from the slides so people actually try to understand what the slides mean– that they are examples but you can’t just mindlessly copy and paste.
I also liked how Shin addressed things related to publications and really developed students questions.
Workshop Details
Prerequisites: None
Length: 3 days, 2 hrs per day
Level: Introductory
Location: Collaboratory Classroom (Boyer Hall, 529)
Seats Available: 10
Winter 2020 Dates
February 18, 19, and 20, 2020
10:00 AM to 12:00 PM